When I plug my phones (I tried 2 models) or CD to "CD/MP3 in" the output signal is very low. The volume through headphones or PA is at least twice low as my guitar signal or usb stream from the computer and it's almost gone when line/amp selector is down (when I turn off boost)...

even more, the vocal sounds nasally and muted, kind of voice-cancel effect, and overall sound is not natural and "closed".

I had a similar issue when I tried a pair of the new Apple earpods (the kind that ship with the iPhone 5). Something just wasn't aligning with the HD jack and things sounded horrible. So I went back to the phones I was using previously.

You mentioned that you used two pairs of phones, so this may not be the issue...unless they happen to be a make/model of phone that doesn't work with the Pod either.